Variant ID: vg0714562076 (JBrowse) | Variation Type: SNP |
Chromosome: chr07 | Position: 14562076 |
Reference Allele: C | Alternative Allele: T |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.07, others allele: 0.00, population size: 213. )
CACAAAGACTCGGGTTGCTCTAATAGCCAACAAACAGGAGGATGTGCACACCTAGCAAAAGACCTTTTGGGAAACAGGGACTTATTCCAAGTACCTGTCA[C/T]
ATCGGATGTTCGGACACTAATTTGAAGTATTAAACATACACTAATTACAAAACCCATTCCATATCCTTGACTAATTCGCGAGACGAATCTTTTGAGTCTA
TAGACTCAAAAGATTCGTCTCGCGAATTAGTCAAGGATATGGAATGGGTTTTGTAATTAGTGTATGTTTAATACTTCAAATTAGTGTCCGAACATCCGAT[G/A]
TGACAGGTACTTGGAATAAGTCCCTGTTTCCCAAAAGGTCTTTTGCTAGGTGTGCACATCCTCCTGTTTGTTGGCTATTAGAGCAACCCGAGTCTTTGTG
Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 92.40% | 7.60% | 0.00% | 0.00% | NA |
All Indica | 2759 | 98.00% | 2.00% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 79.90% | 20.10% | 0.00% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 93.00% | 7.00% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 65.30% | 34.70% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 84.60% | 15.40% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0714562076 | C -> T | LOC_Os07g25450.1 | upstream_gene_variant ; 1185.0bp to feature; MODIFIER | silent_mutation | Average:51.344; most accessible tissue: Zhenshan97 panicle, score: 73.605 | N | N | N | N |
vg0714562076 | C -> T | LOC_Os07g25440-LOC_Os07g25450 | intergenic_region ; MODIFIER | silent_mutation | Average:51.344; most accessible tissue: Zhenshan97 panicle, score: 73.605 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0714562076 | NA | 6.20E-10 | mr1624 | All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
vg0714562076 | NA | 4.31E-10 | mr1624 | Jap_All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
vg0714562076 | NA | 6.32E-09 | mr1624_2 | Jap_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
vg0714562076 | NA | 5.75E-08 | mr1733_2 | Jap_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
vg0714562076 | NA | 1.52E-06 | mr1741_2 | Jap_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
vg0714562076 | NA | 1.85E-06 | mr1887_2 | Jap_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |